SMTL ID : 5bya.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PCP)2-IP4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 21 residues within 4Å: Chain A: R.98, P.113, V.149, K.151, H.158, V.160, L.175, E.201, E.202, F.203, M.204, D.210, S.228, P.229, D.273, L.275, C.284, D.285 Ligands: 4WZ.2, MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.151, A:E.201, A:E.201, A:M.204, A:D.210, A:D.285, A:D.285 Water bridges: A:R.98, A:D.210, A:S.228, A:S.228, A:D.285 Salt bridges: A:R.98, A:R.98, A:K.151, A:H.158

1 x 4WZ: {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)(Non-covalent)

4WZ.2: 16 residues within 4Å: Chain A: K.17, K.18, R.177, K.178, K.212, R.226, D.273, D.285, N.287, S.290, K.293 Ligands: ADP.1, MG.3, MG.4, MG.6, EDO.10 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:K.178, A:D.285 Water bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:K.18, A:R.177, A:R.177, A:R.177, A:K.178, A:K.212, A:K.212, A:D.285, A:N.287, A:N.287, A:S.290, A:S.290, A:S.290 Salt bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:R.177, A:R.177, A:K.178, A:K.212, A:R.226, A:K.293

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.285, N.287 Ligands: ADP.1, 4WZ.2, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.4, H2O.4 MG.4: 5 residues within 4Å: Chain A: D.273, D.285 Ligands: ADP.1, 4WZ.2, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.3 MG.5: 3 residues within 4Å: Chain A: S.32, F.34, I.37 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.34, A:I.37, H2O.4, H2O.12, H2O.13 MG.6: 2 residues within 4Å: Chain A: K.212 Ligands: 4WZ.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: N.287 No protein-ligand interaction detected (PLIP)

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: N.54, W.55, P.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.54 Water bridges: A:L.57 EDO.10: 9 residues within 4Å: Chain A: K.212, V.213, Y.214, G.271, F.272, D.273, N.287, S.290 Ligands: 4WZ.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.272, A:N.287, A:S.290, A:S.290 EDO.11: 7 residues within 4Å: Chain A: N.251, R.253, R.276, A.277, G.279, Q.280, S.281 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.277, A:G.279 Water bridges: A:R.253, A:G.279, A:G.279, A:G.279 EDO.12: 3 residues within 4Å: Chain A: Y.220, H.222, Y.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.301 Water bridges: A:A.221, A:A.223 EDO.14: 4 residues within 4Å: Chain A: F.69, P.70, L.71, D.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.71, A:D.72 Water bridges: A:H.65

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 3 residues within 4Å: Chain A: S.181, R.182, K.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.181 Salt bridges: A:R.182, A:K.234 ACT.13: 1 residues within 4Å: Chain A: F.34 No protein-ligand interaction detected (PLIP) ACT.15: 4 residues within 4Å: Chain A: H.65, Q.92, I.95, Q.96 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.92, A:I.95, A:Q.96 Hydrogen bonds: A:H.65, A:Q.92, A:E.156 Salt bridges: A:H.65 ACT.16: 5 residues within 4Å: Chain A: A.78, V.85, D.88, L.89, N.90 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.90 Hydrogen bonds: A:D.88, A:L.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riley, A.M. et al., Synthetic tools for studying the chemical biology of InsP8. Chem.Commun.(Camb.) (2015)

Release Date

2015-07-22

Peptides

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2

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